SynBioFromLeukipposInstitute

Isoprenoids are an attractive class of metabolites for enzymatic synthesis from renewable substrates. However, metabolic engineering of microorganisms for monoterpenoid production is limited by the need for time-consuming, and often non-intuitive, combinatorial tuning of biosynthetic pathway variations to meet design criteria. Towards alleviating this limitation, the goal of this work was to build a modular, cell-free platform for construction and testing of monoterpenoid pathways, using the fragrance and flavoring molecule limonene as a model. In this platform, multiple Escherichia coli lysates, each enriched with a single overexpressed pathway enzyme, are mixed to construct the full biosynthetic pathway. First, we show the ability to synthesize limonene from six enriched lysates with mevalonate substrate, an adenosine triphosphate (ATP) source, and cofactors. Next, we extend the pathway to use glucose as a substrate, which relies on native metabolism in the extract to convert glucose to acetyl-CoA along with three additional enzymes to convert acetyl-CoA to mevalonate. We find that the native E. coli farnesyl diphosphate synthase (IspA) is active in the lysate and diverts flux from the pathway intermediate geranyl pyrophospahte to farnesyl pyrophsophate and the byproduct farnesol. By adjusting the relative levels of cofactors NAD+, ATP and CoA, the system can synthesize 0.66 mM (90.2 mg l−1) limonene over 24 h, a productivity of 3.8 mg l−1 h−1. Our results highlight the flexibility of crude lysates to sustain complex metabolism and, by activating a glucose-to-limonene pathway with 9 heterologous enzymes encompassing 20 biosynthetic steps, expands an approach of using enzyme-enriched lysates for constructing, characterizing and prototyping enzymatic pathways.

"Control theory, a branch of engineering devoted to the analysis and design of robust systems through feedback control, has been instrumental for many technological applications. It has been proposed that control theory is also a productive framework to analyze biological systems and advance their engineering. Examples confirming this perspective include the design of schemes of biomolecular sequestration to implement integral negative feedback for perfect disturbance rejection and the discovery of control theoretic tradeoffs between stability and performance in the glycolytic pathway in Saccharomyces cerevisiae. Here, we briefly review some concepts and tools from classical feedback control theory that have been invoked in the study of biological systems, and argue for the need to develop new control concepts specifically tailored to biology." https://www.sciencedirect.com/science/article/pii/S2452310019300113

Microsoft just booted up the first “DNA drive” for storing data

Off-target editing could complicate developing safe “base-edited” therapies

A research team led by biophysical chemist Professor Edward Lemke has engineered a designer organelle in a living mammalian cell in a new complex biological translation process. The created membraneless organelle can build proteins from natural and synthetic amino acids carrying new functionalities.

DNA IS SUPPOSED to rescue us from a computing rut. With advances using silicon petering out, DNA-based computers hold the promise of massive parallel computing architectures that are impossible today.

But there’s a problem: The molecular circuits built so far have no flexibility at all. Today, using DNA to compute is “like having to build a new computer out of new hardware just to run a new piece of software,” says computer scientist David Doty. So Doty, a professor at UC Davis, and his colleagues set out to see what it would take to implement a DNA computer that was in fact reprogrammable.

As detailed in a paper published this week in Nature, Doty and his colleagues from Caltech and Maynooth University demonstrated just that. They showed it’s possible to use a simple trigger to coax the same basic set of DNA molecules into implementing numerous different algorithms. Although this research is still exploratory, reprogrammable molecular algorithms could be used in the future to program DNA robots, which have already successfully delivered drugs to cancerous cells.

“This is one of the landmark papers in the field,” says Thorsten-Lars Schmidt, an assistant professor for experimental biophysics at Kent State University who was not involved in the research. “There was algorithmic self-assembly before, but not to this degree of complexity.”

In electronic computers like the one you’re using to read this article, bits are the binary units of information that tell a computer what to do. They represent the discrete physical state of the underlying hardware, usually the presence or absence of an electrical current. These bits, or rather the electrical signals implementing them, are passed through circuits made up of logic gates, which perform an operation on one or more input bits and produce one bit as an output.

Unnatural gene expression imposes a load on engineered microorganisms that decreases their growth and subsequent production yields, a phenomenon known as burden. In the last decade, the field of synthetic biology has made progress on the development of biomolecular feedback control systems and other approaches that can improve the growth of engineered cells, as well as the genetic stability, portability and robust performance of cell-hosted synthetic constructs. In this review, we highlight recent work focused on the development of host-aware synthetic biology. https://www.sciencedirect.com/science/article/pii/S245231001930006X

"In this mini review, we will briefly introduce the rapid development of DNA conformational polymorphism in biosensing field, including canonical DNA duplex, triplex, quadruplex, DNA origami, as well as more functionalized DNAs (aptamer, DNAzyme etc.). Various DNA structuresare adopted to play important roles in sensor construction, through working as recognition receptor, signal reporter or linking staple for signal motifs, etc. We will mainly summarize their recent developments in DNA-based electrochemical and fluorescent sensors. For the electrochemical sensors, several types will be included, e.g. the amperometric, electrochemical impedance, electrochemiluminescence, as well as field-effect transistor sensors. For the fluorescent sensors, DNA is usually modified with fluorescent molecules or novel nanomaterials as report probes, excepting its core recognition function. Finally, general conclusion and future perspectives will be discussed for further developments."

https://www.sciencedirect.com/science/article/pii/S0956566319301216?dgcid=raven_sd_via_email